stc1 (SPBP8B7.28c)


Gene Standard Namestc1 Characterisation Statuspublished
Systematic IDSPBP8B7.28c Feature Typeprotein coding
Synonyms Name DescriptionSiRNA To Chromatin
ProductLIM-like protein linking chromatin modification to RNAi, Stc1 Product Size215aa, 25.07 kDa
Genomic Location Chromosome II, 3691942-3691008 (935nt); CDS:3691848-3691201 (648nt)

Ensembl Gene Location
GO Molecular Function
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0005515protein bindingIPIago1PMID:20211136865
GO Biological Process
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0044382CLRC ubiquitin ligase complex localization to heterochromatin2
localizes CLRC ubiquitin ligase complexIMPPMID:20211136
GO:0030702chromatin silencing at centromereIMPPMID:2021113653
GO:0031048chromatin silencing by small RNAIMPPMID:2021113620
GO:0035389establishment of chromatin silencing at silent mating-type cassetteIMPPMID:202111362
GO:0035390establishment of chromatin silencing at telomereIMPPMID:202111361
GO:0007126meiotic nuclear divisionIEAUniProtKB-KW:KW-0469GO_REF:0000037330
GO:0051570regulation of histone H3-K9 methylationIMPPMID:2021113613
GO Cellular Component
Term IDTerm NameEvidenceWith/FromReferenceCount
GO:0043494CLRC ubiquitin ligase complexIDAPMID:202111367
GO:0031618nuclear pericentric heterochromatin38
localization requires chromatin silencing by small RNAIDAPMID:20211136
GO:0005730nucleolusIDAPMID:16823372357
GO:0005634nucleusIDAPMID:168233722737
Fission Yeast Phenotype Ontology

Population Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0001701sensitive to bortezomib256
expressivity FYPO_EXT:0000003Cell growth assaystc1ΔNullPECO:0000005, PECO:0000137PMID:21760946
FYPO:0000085sensitive to camptothecincompetitive growth assay evidencestc1ΔNullPMID:20537132211
FYPO:0000091sensitive to thiabendazolecompetitive growth assay evidencestc1ΔNullPMID:20537132175
FYPO:0002060viable vegetative cell populationMicroscopystc1ΔNullPMID:204732893751
Microscopystc1ΔNullPECO:0000005, PECO:0000137PMID:23697806

Cell Phenotype

Term IDTerm NameEvidenceAlleleExpressionConditionReferenceCount
FYPO:0000190abnormal actin cortical patch localizationMicroscopystc1ΔNullPMID:2369780650
FYPO:0002398abnormal actin cytoskeletonMicroscopystc1ΔNullPMID:2369780645
FYPO:0000029abnormal chromosome segregationnot recorded (unrecorded)PMID:20211136178
FYPO:0000051abnormal meiosisMicroscopystc1ΔNullPMID:1616948995
FYPO:0000273centromeric outer repeat transcripts absentnot recorded (unrecorded)PMID:202111367
FYPO:0000227chromosome loss during mitotic chromosome segregationnot recorded (unrecorded)PMID:202111367
FYPO:0000220increased centromeric outer repeat transcript levelnot recorded (unrecorded)PMID:2021113615
FYPO:0000228lagging mitotic chromosomesMicroscopynot recorded (unrecorded)PMID:2021113613
FYPO:0002112viable curved vegetative cell59
penetrance FYPO_EXT:0000003Microscopystc1ΔNullPECO:0000005, PECO:0000137PMID:23697806
Transcript
Ensembl transcript structure with UTRs, exons and introns

Exons

Exon Start End
136919423691008
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF12898 Pfam IPR024630 Stc1 domain 41 122 1

View domain organization at Pfam

Protein Properties

Ave. residue weight 116.63 Da
Charge -3.00
Isoelectric point 5.69
Molecular weight 25.07 kDa
Number of residues 215
Modifications

Protein Modifications

Term IDTerm NameEvidenceResidueReferenceCount
MOD:00046O-phospho-L-serineS146PMID:247631071670
present during mitotic M phaseS169PMID:21712547
present during mitotic M phaseS146PMID:21712547
MOD:00047O-phospho-L-threonineT172PMID:21712547690
present during mitotic M phase
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
NDduring GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
NDduring cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
0.67during GO:0072690PECO:0000005,
PECO:0000014
population_wideexperimental evidencePMID:23101633
0.2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population_wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog601
conserved in fungi only620
conserved in fungi4599
Orthologs

Orthologs in Compara


Genetic Interactions

Source: BioGRID

Gene Product Evidence Reference
trm10tRNA m(1)G methyltransferase Trm10 Positive GeneticPMID:22681890
SPAC343.04cWD repeat protein, human WDR26 family, ubiquitin ligase complex subunit (predicted) Negative GeneticPMID:22681890
cdt2WD repeat protein Cdt2 Negative GeneticPMID:22681890
rik1silencing protein Rik1 Phenotypic SuppressionPMID:20211136
Positive GeneticPMID:22681890
clr4histone H3 lysine methyltransferase Clr4 Phenotypic SuppressionPMID:20211136
Positive GeneticPMID:22681890
toe2transcription factor, zf-fungal binuclear cluster type (predicted) Negative GeneticPMID:22681890
sap14U2 snRNP-associated protein SF3B14 Sap14 Negative GeneticPMID:22681890
swd1Set1C complex subunit Swd1 Positive GeneticPMID:22681890
sfp1transcription factor Sfp1 (predicted) Negative GeneticPMID:22681890
raf2Rik1-associated factor Raf2 Phenotypic SuppressionPMID:20211136
Positive GeneticPMID:22681890
par2protein phosphatase regulatory subunit Par2 Positive GeneticPMID:22681890
ers1RNA-silencing factor Ers1 Positive GeneticPMID:22681890
eso1sister chromatid cohesion protein/DNA polymerase eta Eso1 fusion protein Negative GeneticPMID:23050226
rad57RecA family ATPase Rad57/Rhp57 Positive GeneticPMID:22681890
dsk1SR protein-specific kinase Dsk1 Positive GeneticPMID:22681890
top1DNA topoisomerase I Positive GeneticPMID:22681890
vrp1verprolin Positive GeneticPMID:22681890
laf1clr6 L associated factor 1 Laf1 Negative GeneticPMID:22681890
raf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Phenotypic SuppressionPMID:20211136
SPCC162.11curidine kinase/uracil phosphoribosyltransferase (predicted) Positive GeneticPMID:22681890
nsk1Clp1-interacting, microtubule plus-end binding Nsk1 Negative GeneticPMID:22681890
cyp7cyclophilin family peptidyl-prolyl cis-trans isomerase Cyp7 (predicted) Negative GeneticPMID:22681890
fft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive GeneticPMID:22681890
mst2histone acetyltransferase Mst2 Synthetic RescuePMID:21289066
hhp2serine/threonine protein kinase Hhp2 Positive GeneticPMID:22681890
sir2Sir2 family histone deacetylase Sir2 Phenotypic SuppressionPMID:20211136
Physical Interactions

Source: BioGRID

Gene Product Evidence Reference
ned8ubiquitin-like protein modifier Ned8 Affinity Capture-MSPMID:20211136
ebp2rRNA processing protein Ebp2 (predicted) Affinity Capture-MSPMID:20211136
SPAC1F12.07phosphoserine aminotransferase (predicted) Affinity Capture-MSPMID:20211136
raf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Affinity Capture-WesternPMID:23613586
Affinity Capture-WesternPMID:20211136
Affinity Capture-MS
mas5DNAJ domain protein Mas5 (predicted) Affinity Capture-MSPMID:20211136
rik1silencing protein Rik1 Affinity Capture-WesternPMID:23613586
Affinity Capture-MSPMID:20211136
Affinity Capture-Western
Affinity Capture-WesternPMID:22319459
Reconstituted ComplexPMID:24449894
raf2Rik1-associated factor Raf2 Affinity Capture-WesternPMID:23613586
Affinity Capture-MSPMID:20211136
Affinity Capture-Western
Reconstituted ComplexPMID:24449894
stc1LIM-like protein linking chromatin modification to RNAi, Stc1 Affinity Capture-MSPMID:20211136
ago1argonaute Reconstituted ComplexPMID:23613586
Affinity Capture-WesternPMID:20211136
Reconstituted Complex
SPAC23G3.06U3 snoRNP protein Nop58 (predicted) Affinity Capture-MSPMID:20211136
clr4histone H3 lysine methyltransferase Clr4 Affinity Capture-WesternPMID:23613586
Affinity Capture-WesternPMID:20211136
ers1RNA-silencing factor Ers1 Affinity Capture-WesternPMID:22733737
pcu4cullin 4 Affinity Capture-MSPMID:20211136
SPBC646.10cU3 snoRNP protein Nop56 (predicted) Affinity Capture-MSPMID:20211136
External References
Database Identifier Description
NBRP SPBP8B7.28c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBP8B7.28c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBP8B7.28c BioGRID Interaction Datasets
Expression Viewer SPBP8B7.28c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBP8B7.28c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBP8B7.28c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBP8B7.28c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBP8B7.28c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBP8B7.28c Transcriptome Viewer (Bähler Lab)
Cyclebase SPBP8B7.28c Cell Cycle Data
GEO SPBP8B7.28c GEO profiles
PInt SPBP8B7.28c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBP8B7.28c Peptides identified in tandem mass spectrometry proteomics experiments
SPD / RIKEN07/07D12Orfeome Localization Data
UniProtKB/SwissProtO94276Meiotic chromosome segregation protein P8B7.28c
ModBaseO94276Database of comparative protein structure models
STRINGO94276Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596535LIM-like protein linking chromatin modification to RNAi, Stc1
RefSeq mRNANM_001022456972h- LIM-like protein linking chromatin modification to RNAi, Stc1 (stc1), mRNA
ePDB2LUYThe European PDB
PDB2LUYPDB
PDBsum2LUYPDBsum
European Nucleotide ArchiveCAA21813.1ENA Protein Mapping
UniParcUPI000006B57EUniProt Archive

Literature for stc1

Search: Europe PMC or PubMed

Release Version: PomBase:23_46 - 30 Aug 2014